MIR3127 (microRNA 3127) - Rat Genome Database

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Gene: MIR3127 (microRNA 3127) Homo sapiens
Analyze
Symbol: MIR3127
Name: microRNA 3127
RGD ID: 4108991
HGNC Page HGNC:38269
Description: microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]
Type: ncrna (Ensembl: miRNA)
RefSeq Status: PROVISIONAL
Previously known as: mir-3127
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38296,798,278 - 96,798,353 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl296,798,278 - 96,798,353 (+)EnsemblGRCh38hg38GRCh38
GRCh37297,464,015 - 97,464,090 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera291,904,180 - 91,904,255 (+)NCBICelera
Cytogenetic Map2q11.2NCBI
HuRef291,424,775 - 91,424,850 (+)NCBIHuRef
CHM1_1297,468,919 - 97,468,994 (+)NCBICHM1_1
T2T-CHM13v2.0297,304,908 - 97,304,983 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
schizophrenia  (IAGP)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Schizophrenia  (IAGP)
References
Additional References at PubMed
PMID:16381832   PMID:20300190   PMID:21037258   PMID:21199797   PMID:25284075   PMID:25849943   PMID:28351032   PMID:29566281   PMID:30317610   PMID:31942724   PMID:32522016   PMID:34226413  
PMID:34898354   PMID:34978042  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2q11.1-11.2(chr2:95493468-96977610)x3 copy number gain See cases [RCV000133839] Chr2:95493468..96977610 [GRCh38]
Chr2:96159216..97643347 [GRCh37]
Chr2:95522943..97007074 [NCBI36]
Chr2:2q11.1-11.2		 uncertain significance
GRCh38/hg38 2q11.1-11.2(chr2:95879602-97029672)x3 copy number gain See cases [RCV000050366] Chr2:95879602..97029672 [GRCh38]
Chr2:96545350..97695409 [GRCh37]
Chr2:95909077..97059136 [NCBI36]
Chr2:2q11.1-11.2		 uncertain significance
GRCh38/hg38 2q11.1-11.2(chr2:95879602-97029672)x1 copy number loss See cases [RCV000134141] Chr2:95879602..97029672 [GRCh38]
Chr2:96545350..97695409 [GRCh37]
Chr2:95909077..97059136 [NCBI36]
Chr2:2q11.1-11.2		 pathogenic
GRCh38/hg38 2q11.2(chr2:96073560-97062710)x1 copy number loss See cases [RCV000135343] Chr2:96073560..97062710 [GRCh38]
Chr2:96739308..97728447 [GRCh37]
Chr2:96103035..97092174 [NCBI36]
Chr2:2q11.2		 pathogenic
GRCh38/hg38 2q11.2(chr2:96100812-97154835)x1 copy number loss See cases [RCV000137012] Chr2:96100812..97154835 [GRCh38]
Chr2:96766560..97820572 [GRCh37]
Chr2:96130287..97184299 [NCBI36]
Chr2:2q11.2		 uncertain significance
GRCh38/hg38 2q11.1-11.2(chr2:95337458-99072953)x3 copy number gain See cases [RCV000138012] Chr2:95337458..99072953 [GRCh38]
Chr2:96003206..99689416 [GRCh37]
Chr2:95366933..99055848 [NCBI36]
Chr2:2q11.1-11.2		 uncertain significance
GRCh38/hg38 2q11.1-11.2(chr2:95766541-97589743)x3 copy number gain See cases [RCV000137817] Chr2:95766541..97589743 [GRCh38]
Chr2:96432289..98206206 [GRCh37]
Chr2:95796016..97572638 [NCBI36]
Chr2:2q11.1-11.2		 uncertain significance
GRCh38/hg38 2q11.1-13(chr2:94678532-110602409)x3 copy number gain See cases [RCV000141075] Chr2:94678532..110602409 [GRCh38]
Chr2:95344257..111359986 [GRCh37]
Chr2:94707984..111076455 [NCBI36]
Chr2:2q11.1-13		 pathogenic
GRCh38/hg38 2q11.2(chr2:96066771-97285797)x3 copy number gain See cases [RCV000142146] Chr2:96066771..97285797 [GRCh38]
Chr2:96732519..98079569 [GRCh37]
Chr2:96096246..97432433 [NCBI36]
Chr2:2q11.2		 uncertain significance
GRCh38/hg38 2q11.2(chr2:96100816-97285797)x3 copy number gain See cases [RCV000142814] Chr2:96100816..97285797 [GRCh38]
Chr2:96766564..98013954 [GRCh37]
Chr2:96130291..97380093 [NCBI36]
Chr2:2q11.2		 uncertain significance
GRCh38/hg38 2q11.2(chr2:96073560-97513144)x1 copy number loss See cases [RCV000142800] Chr2:96073560..97513144 [GRCh38]
Chr2:96739308..98066294 [GRCh37]
Chr2:96103035..97496039 [NCBI36]
Chr2:2q11.2		 pathogenic
GRCh38/hg38 2q11.2(chr2:96073560-97589743)x3 copy number gain See cases [RCV000143142] Chr2:96073560..97589743 [GRCh38]
Chr2:96739308..98206206 [GRCh37]
Chr2:96103035..97572638 [NCBI36]
Chr2:2q11.2		 likely benign
GRCh38/hg38 2q11.1-11.2(chr2:95879602-97285797)x1 copy number loss See cases [RCV000051260] Chr2:95879602..97285797 [GRCh38]
Chr2:96545350..98013866 [GRCh37]
Chr2:95909077..97380005 [NCBI36]
Chr2:2q11.1-11.2		 pathogenic
GRCh38/hg38 2q11.2(chr2:96100812-97285797)x1 copy number loss See cases [RCV000051137] Chr2:96100812..97285797 [GRCh38]
Chr2:96766560..98013866 [GRCh37]
Chr2:96130287..97380005 [NCBI36]
Chr2:2q11.2		 pathogenic
GRCh38/hg38 2p11.2-q11.2(chr2:91443218-102334856)x3 copy number gain See cases [RCV000052945] Chr2:91443218..102334856 [GRCh38]
Chr2:91617683..102951316 [GRCh37]
Chr2:90981410..102317748 [NCBI36]
Chr2:2p11.2-q11.2		 pathogenic
GRCh38/hg38 2q11.1-12.1(chr2:94817406-103252396)x3 copy number gain See cases [RCV000052946] Chr2:94817406..103252396 [GRCh38]
Chr2:95618109..103868854 [GRCh37]
Chr2:94846878..103235286 [NCBI36]
Chr2:2q11.1-12.1		 pathogenic
GRCh38/hg38 2q11.1-11.2(chr2:95806265-97285797)x3 copy number gain See cases [RCV000053136] Chr2:95806265..97285797 [GRCh38]
Chr2:96472013..98013866 [GRCh37]
Chr2:95835740..97380005 [NCBI36]
Chr2:2q11.1-11.2		 uncertain significance
GRCh38/hg38 2q11.1-11.2(chr2:95810453-97024341)x3 copy number gain See cases [RCV000053137] Chr2:95810453..97024341 [GRCh38]
Chr2:96476201..97690078 [GRCh37]
Chr2:95839928..97053805 [NCBI36]
Chr2:2q11.1-11.2		 uncertain significance
GRCh38/hg38 2q11.1-11.2(chr2:95880668-97131646)x3 copy number gain See cases [RCV000053138] Chr2:95880668..97131646 [GRCh38]
Chr2:96546416..97797383 [GRCh37]
Chr2:95910143..97161110 [NCBI36]
Chr2:2q11.1-11.2		 uncertain significance
GRCh38/hg38 2q11.1-11.2(chr2:95916534-97024341)x3 copy number gain See cases [RCV000053139] Chr2:95916534..97024341 [GRCh38]
Chr2:96582282..97690078 [GRCh37]
Chr2:95946009..97053805 [NCBI36]
Chr2:2q11.1-11.2		 uncertain significance
GRCh38/hg38 2q11.2(chr2:96100612-97285797)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053140]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053140]|See cases [RCV000053140] Chr2:96100612..97285797 [GRCh38]
Chr2:96766360..98014007 [GRCh37]
Chr2:96130087..97380146 [NCBI36]
Chr2:2q11.2		 uncertain significance
NC_000002.12:g.(?_96063558)_(97079140_?)del deletion Schizophrenia [RCV000754268] Chr2:96063558..97079140 [GRCh38]
Chr2:2q11.2		 likely pathogenic
miRNA Target Status

Confirmed Targets
Gene TargetMature miRNAMethod NameResult TypeData TypeSupport TypePMID
SLC22A23hsa-miR-3127-5pMirtarbaseexternal_infoCLASHFunctional MTI (Weak)23622248

Predicted Targets
Summary Value
Count of predictions:66513
Count of gene targets:18591
Count of transcripts:47895
Interacting mature miRNAs:hsa-miR-3127-3p, hsa-miR-3127-5p
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 1 16 1 5
Low 118 20 62 36 267 39 98 42 86 61 127 153 3 3 21 2
Below cutoff 23 14 12 2 24 2 26 25 17 10 12 24 1 3 10 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000583925
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl296,798,278 - 96,798,353 (+)Ensembl
RefSeq Acc Id: NR_036074
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38296,798,278 - 96,798,353 (+)NCBI
GRCh37297,464,015 - 97,464,090 (+)RGD
Celera291,904,180 - 91,904,255 (+)RGD
HuRef291,424,775 - 91,424,850 (+)ENTREZGENE
CHM1_1297,468,919 - 97,468,994 (+)NCBI
T2T-CHM13v2.0297,304,908 - 97,304,983 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC MIR3127 COSMIC
Ensembl Genes ENSG00000264157 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000583925 ENTREZGENE
GTEx ENSG00000264157 GTEx
HGNC ID HGNC:38269 ENTREZGENE
Human Proteome Map MIR3127 Human Proteome Map
miRBase MI0014144 ENTREZGENE
NCBI Gene 100422928 ENTREZGENE
PharmGKB PA165696808 PharmGKB
RNAcentral URS0000170D8B RNACentral
  URS0000292363 RNACentral
  URS000075DB87 RNACentral